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Vienna and Prague

A friend and I will be flying roundtrip to Vienna in mid-Oct for one week. We have planned to take the train to Prague and back to Vienna in time to catch our flight. It would be approx. 3 days in each city. Is that enough time? We aren't too into museums, we would rather walk around the city and just sort of tumble into different things. Can anyone recommend good (reasonable) hotels in both cities? If it has wifi, breakfast and close to subway/tram/bus and does not exceed $100 a night for 2 people, we would be grateful. Any ideas would be appreciated.

Also, is mid-oct a good time to go? It's the only time we can get off of work for a week.